BASiCStan-package: The 'BASiCStan' package.

In Alanocallaghan/BASiCStan: Stan implementation of BASiCS

The 'BASiCStan' package.

Description

Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries. See also BASiCS_MCMC

References

Stan Development Team (2020). RStan: the R interface to Stan. R package version 2.21.2. https://mc-stan.org

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1004333.

Vallejos, Richardson and Marioni (2016). Genome Biology. https://doi.org/10.1186/s13059-016-0930-3

Eling et al (2018). Cell Systems. https://doi.org/10.1016/j.cels.2018.06.011

Alanocallaghan/BASiCStan documentation built on Feb. 19, 2024, 10:40 p.m.